SMTL ID : 7m1i.1 (1 other biounit)

Crystal structure of dehaloperoxidase B in complex with 2,6-dichlorophenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 19 residues within 4Å: Chain A: F.24, E.31, N.34, F.35, H.55, K.58, V.59, L.62, M.63, L.83, M.86, Q.88, H.89, L.92, N.96, F.97, L.100, L.127 Ligands: DUB.2 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:F.24, A:F.35, A:K.58, A:V.59, A:L.62, A:M.63, A:L.83, A:Q.88, A:L.92, A:N.96, A:F.97, A:L.100, A:L.127 Salt bridges: A:H.55, A:H.55, A:K.58 Metal complexes: A:H.89

1 x DUB: 2,6-dichlorophenol(Non-covalent)

DUB.2: 8 residues within 4Å: Chain A: F.21, F.35, Y.38, F.52, H.55, T.56, V.59 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.21, A:V.59 Hydrogen bonds: A:Y.38, A:Y.38 pi-Stacking: A:F.35 Halogen bonds: A:T.56

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.26, A:D.43 GOL.4: 4 residues within 4Å: Chain A: R.10, E.65, D.68, R.69 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.10, A:R.10, A:D.68, A:D.68, A:R.69

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: G.1, F.2, K.3, D.116 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.1, A:F.2, A:K.3 Water bridges: A:Q.4, A:D.116, A:S.119, A:S.119 SO4.6: 3 residues within 4Å: Chain A: K.32, V.39, G.40 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.40 Water bridges: A:K.32, A:K.32 Salt bridges: A:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malewschik, T. et al., Bridging the functional gap between reactivity and inhibition in dehaloperoxidase B from Amphitrite ornata: Mechanistic and structural studies with 2,4- and 2,6-dihalophenols. J.Inorg.Biochem. (2022)

Release Date

2022-08-17

Peptides

Dehaloperoxidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dehaloperoxidase B

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